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GeneBe

19-4543904-C-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_032108.4(SEMA6B):c.2364G>C(p.Pro788=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000474 in 1,202,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00027 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000016 ( 0 hom. )

Consequence

SEMA6B
NM_032108.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.555
Variant links:
Genes affected
SEMA6B (HGNC:10739): (semaphorin 6B) This gene encodes a member of the semaphorin family, a group of proteins characterized by the presence of a conserved semaphorin (sema) domain. Whereas some semaphorins are transmembrane proteins, others are secreted. Semaphorins play a major role in axon guidance. The protein encoded by this gene may be involved in both peripheral and central nervous system development. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 19-4543904-C-G is Benign according to our data. Variant chr19-4543904-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 792322.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.555 with no splicing effect.
BS2
High AC in GnomAd at 40 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SEMA6BNM_032108.4 linkuse as main transcriptc.2364G>C p.Pro788= synonymous_variant 17/17 ENST00000586582.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SEMA6BENST00000586582.6 linkuse as main transcriptc.2364G>C p.Pro788= synonymous_variant 17/171 NM_032108.4 P1Q9H3T3-1
SEMA6BENST00000586965.1 linkuse as main transcriptc.1851+513G>C intron_variant 1 Q9H3T3-3
SEMA6BENST00000676793.1 linkuse as main transcriptc.2364G>C p.Pro788= synonymous_variant 17/17 P1Q9H3T3-1
SEMA6BENST00000677828.1 linkuse as main transcriptc.*1626G>C 3_prime_UTR_variant, NMD_transcript_variant 17/17

Frequencies

GnomAD3 genomes
AF:
0.000266
AC:
40
AN:
150210
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000928
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000133
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000162
AC:
17
AN:
1051910
Hom.:
0
Cov.:
33
AF XY:
0.0000201
AC XY:
10
AN XY:
496362
show subpopulations
Gnomad4 AFR exome
AF:
0.000691
Gnomad4 AMR exome
AF:
0.000134
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000241
GnomAD4 genome
AF:
0.000266
AC:
40
AN:
150314
Hom.:
0
Cov.:
32
AF XY:
0.000286
AC XY:
21
AN XY:
73422
show subpopulations
Gnomad4 AFR
AF:
0.000925
Gnomad4 AMR
AF:
0.000133
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.000378

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
6.2
Dann
Benign
0.82

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs868549018; hg19: chr19-4543916; API